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base repository: levitsky/pyteomics
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base: v4.6
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head repository: levitsky/pyteomics
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compare: master
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Commits on May 12, 2023

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Commits on Jun 13, 2023

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Commits on Jun 16, 2023

  1. Update changelog

    levitsky committed Jun 16, 2023
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Commits on Aug 9, 2023

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Commits on Aug 11, 2023

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  2. Merge pull request #117 from markmipt/master

    Add optional quantile regression for get_RCs
    levitsky authored Aug 11, 2023
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Commits on Aug 30, 2023

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  4. Fix syntax

    levitsky committed Aug 30, 2023
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  5. Fix command

    levitsky committed Aug 30, 2023
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  6. Fix command

    levitsky committed Aug 30, 2023
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Commits on Aug 31, 2023

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Commits on Sep 1, 2023

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  3. Fixing tests

    caetera committed Sep 1, 2023
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Commits on Sep 3, 2023

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Commits on Sep 4, 2023

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Commits on Sep 5, 2023

  1. Merge pull request #120 from caetera/fasta_description

    Add raw fasta file header to parsers
    levitsky authored Sep 5, 2023
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  2. Changelog update

    levitsky committed Sep 5, 2023
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  4. add .readthedocs.yaml

    levitsky committed Sep 5, 2023
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  5. Fix typo

    levitsky committed Sep 5, 2023
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  7. Fixes for newer sphinx

    levitsky committed Sep 5, 2023
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Commits on Sep 6, 2023

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Commits on Sep 7, 2023

  1. Merge pull request #121 from levitsky/metaclass_add_init

    Use metaclass to add __init__ to flavored fasta parsers
    levitsky authored Sep 7, 2023
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  2. Version 4.6.2

    levitsky committed Sep 7, 2023
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  3. Fix typo in changelog

    levitsky committed Sep 7, 2023
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Commits on Sep 8, 2023

  1. Fix #122

    levitsky committed Sep 8, 2023
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Commits on Sep 11, 2023

  1. Fix #124

    sjust-seerbio authored Sep 11, 2023
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  3. Update changelog

    levitsky committed Sep 11, 2023
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Commits on Sep 19, 2023

  1. Update imports for sqlalchemy v2.0 changes

    In sqlalchemy version 2.0, `declarative_base` and `DeclarativeMeta` moved to another module. This adds a try-except around the imports to retain compatibility with sqlalchemy <2.0 and >2.0. Before, the import still worked, but resulted in `MovedIn20Warning` (for example: https://github.com/compomics/psm_utils/actions/runs/6239222484/job/16936699966?pr=50#step:7:35)
    RalfG authored Sep 19, 2023
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Commits on Oct 10, 2023

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  2. Re-factor name retrieval

    mobiusklein committed Oct 10, 2023
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Commits on Oct 13, 2023

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Commits on Oct 17, 2023

  1. Merge pull request #129 from mobiusklein/feature/use_psims_unimod_if_…

    …available
    
    If psims is available, use its Unimod because it caches and vendors
    levitsky authored Oct 17, 2023
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Commits on Nov 1, 2023

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Commits on Nov 2, 2023

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  2. Merge pull request #130 from mobiusklein/fix/mass_mod_hashing

    Mass modification hashing
    levitsky authored Nov 2, 2023
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  4. Update workflows

    levitsky committed Nov 2, 2023
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Commits on Nov 8, 2023

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Commits on Dec 1, 2023

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  3. Check warnings

    mobiusklein committed Dec 1, 2023
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  4. Merge pull request #133 from mobiusklein/fix/more_unimod_fixes

    Fix UniMod by ID
    levitsky authored Dec 1, 2023
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26 changes: 23 additions & 3 deletions .github/workflows/pythonpackage.yml
Original file line number Diff line number Diff line change
@@ -16,12 +16,12 @@ jobs:
runs-on: 'ubuntu-20.04'
strategy:
matrix:
python-version: ['2.7', '3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
@@ -31,6 +31,26 @@ jobs:
python -m pip install --upgrade pip
pip install numpy
pip install -r test-requirements.txt
pip install .
- name: Run the tests
run: |
cd tests; find . -name 'test_*.py' -print0 | xargs -0 -n1 python
tests-py2:
runs-on: 'ubuntu-20.04'
container:
image: python:2.7.18-buster
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
apt-get update
apt-get install -y --no-install-recommends libhdf5-serial-dev
python -m pip install --upgrade pip
pip install numpy
pip install -r test-requirements.txt
- name: Print Python version
run: python -V
- name: Run the tests
run: |
cd tests; find . -name 'test_*.py' -print0 | xargs -0 -n1 env PYTHONPATH=.. python
4 changes: 2 additions & 2 deletions .github/workflows/pythonpublish.yml
Original file line number Diff line number Diff line change
@@ -8,9 +8,9 @@ jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: '3.x'
- name: Install dependencies
18 changes: 18 additions & 0 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
# Read the Docs configuration file for Sphinx projects
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

version: 2

build:
os: ubuntu-22.04
tools:
python: "3"

sphinx:
configuration: doc/source/conf.py

python:
install:
- requirements: doc/build-requirements.txt
- method: pip
path: .
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